A5043213807- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Gene Regulatory Network Analysis
- Legume Nitrogen Fixing Symbiosis
- Plant nutrient uptake and metabolism
- Agronomic Practices and Intercropping Systems
- Advanced Data Storage Technologies
- Single-cell and spatial transcriptomics
- Plant and fungal interactions
- Plant-Microbe Interactions and Immunity
- Scientific Computing and Data Management
- Molecular Biology Techniques and Applications
- Autism Spectrum Disorder Research
- Bioenergy crop production and management
- Cell Image Analysis Techniques
- Biofuel production and bioconversion
- Cancer-related molecular mechanisms research
- Cloud Data Security Solutions
- Cancer Genomics and Diagnostics
- Machine Learning in Bioinformatics
- Plant Genetic and Mutation Studies
- Recommender Systems and Techniques
- Coastal wetland ecosystem dynamics
- Virology and Viral Diseases
- Computational and Text Analysis Methods
Clemson University
2016-2025
Center for Human Genetics
2019-2024
Greenwood Genetic Center
2022-2024
Legumes establish a symbiotic relationship with nitrogen-fixing rhizobia by developing nodules. Nodules are modified lateral roots that undergo changes in their cellular development response to bacteria, but the transcriptional reprogramming occurs these root cells remains largely uncharacterized. Here, we describe cell-type-specific transcriptome of Medicago truncatula during early nodule wild-type genotype Jemalong A17, complemented hypernodulating mutant (sunn-4) expand cell population...
Effective improvement in sorghum crop development necessitates a genomics-based approach to identify functional genes and QTLs. Sequenced 2009, comprehensive annotation of the genome genomics resources is key enable discovery deployment regulatory metabolic gene networks for improvement. This study utilizes first commercially available whole-transcriptome microarray (Sorgh-WTa520972F) tissue genotype-specific expression patterns all identified Sorghum bicolor exons UTRs. The genechip...
For lignocellulosic bioenergy to become a viable alternative traditional energy production methods, rapid increases in conversion efficiency and biomass yield must be achieved. Increased productivity can achieved through concomitant gains processing as well genetic improvement of feedstock that have the potential for at an industrial scale. The purpose this review is explore genomic resource landscape specific group, C4 grasses. First, grass traits relevant biochemical are examined. Then we...
The study of gene relationships and their effect on biological function phenotype is a focal point in systems biology. Gene co-expression networks built using microarray expression profiles are one technique for discovering interpreting relationships. A knowledge-independent thresholding technique, such as Random Matrix Theory (RMT), useful identifying meaningful Highly connected genes the thresholded network then grouped into modules that provide insight collective functionality. While it...
Abstract Mechanistic models of how single cells respond to different perturbations can help integrate disparate big data sets or predict response varied drug combinations. However, the construction and simulation such have proved challenging. Here, we developed a python-based model creation pipeline that converts few structured text files into an SBML standard is high-performance- cloud-computing ready. We applied this our large-scale, mechanistic pan-cancer signaling (named SPARCED)...
Abstract Introduction: Genes involved in centrosome function, microtubule dynamics, and mitotic regulation are critical for normal cell division. In cancer, dysregulation of these processes can lead to chromosomal instability tumor progression. The genes CEP72, HAUS4, TUBGCP4, HAUS2, PLK1, OFD1 play essential roles cycle regulation, mitosis, particularly spindle assembly function. These interconnected cellular related progression, their altered expression may be linked cancer progression...
Abstract Homo sapiens and Neanderthals underwent hybridization during the Middle/Upper Paleolithic age, culminating in retention of small amounts Neanderthal-derived DNA modern human genome. In current study, we address potential roles Neanderthal single nucleotide polymorphisms (SNP) may be playing autism susceptibility samples black non-Hispanic, white Hispanic, non-Hispanic people using data from Simons Foundation Powering Autism Research (SPARK), Genotype-Tissue Expression (GTEx), 1000...
Given the complex relationship between gene expression and phenotypic outcomes, computationally efficient approaches are needed to sift through large high-dimensional datasets in order identify biologically relevant biomarkers. In this report, we describe a method of identifying most salient biomarker genes dataset, which call "candidate genes", by evaluating ability combinations classify samples from "classification potential". Our algorithm, Gene Oracle, uses neural network test user...
We report a public resource for examining the spatiotemporal RNA expression of 54,893
Abstract The remarkable flexibility and adaptability of generative adversarial networks (GANs) have led to the proliferation its models in bioinformatics research. Proteomic transcriptomic profiles been shown be promising methods for discovering identifying disease biomarkers. However, those analyses were performed by trained human examiners making process tedious, time consuming, hard standardize. With development GANs, it is now possible reduce computational costs analysis produce...
The ability to centralize and store data for long periods on an end user's computational resources is increasingly difficult many scientific disciplines. For example, genomics large distributed, the needs be moved into workflow execution sites ranging from lab workstations cloud. However, typical user not always informed emerging network technology or most efficient methods move share data. Thus, defaults using inefficient transfer across commercial internet.To accelerate transfer, we...
Abstract Admixture refers to the mixing of genetic ancestry from different populations. is important for genomic medicine because it can affect how an individual responds certain medications, they metabolize drugs, and susceptibility diseases. For example, some variants associated with drug metabolism response may be more common in populations, individuals admixed have a frequency these than ancestral Understanding patterns admixture population also help researchers identify new diseases or...
Tumors exhibit complex patterns of aberrant gene expression. Using a knowledge-independent, noise-reducing co-expression network construction software called KINC, we created multiple RNAseq-based networks relevant to brain and glioblastoma biology. In this report, describe the discovery validation glioblastoma-specific module that contains 22 co-expressed genes. The genes are upregulated in relative normal lower grade glioma samples; they also hypo-methylated tumors. Among proneural,...
With the continued rise of scientific computing and enormous increases in size data being processed, scientists must consider whether processes for transmitting storing sufficiently assure integrity data. When is not preserved, computations can fail result increased computational cost due to reruns, or worse, results be corrupted a manner apparent scientist produce invalid science results. Technologies such as TCP checksums, encrypted transfers, checksum validation, RAID erasure coding...
Abstract Autism Spectrum Disorder (ASD) is a complex neurodevelopmental disorder characterized by challenges in social communication as well repetitive or restrictive behaviors. Many genetic associations with ASD have been identified, but most occur fraction of the population. Here, we searched for eQTL-associated DNA variants significantly different allele distributions between ASD-affected and control. Thirty significant associated 174 tissue-specific eQTLs from individuals SPARK project...
Abstract Identification of genes and pathways involved in diseases physiological conditions is a major task systems biology. In this study, we developed novel non‐parameter Ising model to integrate protein–protein interaction network microarray data for identifying differentially expressed (DE) genes. We also proposed simulated annealing algorithm find the optimal configuration model. The was applied two breast cancer sets. results showed that more cancer‐related DE sub‐networks were...
Abstract We report a public resource for examining the spatiotemporal RNA expression of 54,893 M. truncatula genes during first 72 hours response to rhizobial inoculation. Using methodology that allows synchronous inoculation and growth over 100 plants in single media container, we harvested same segment each root responding rhizobia initial time course, collected individual tissues from these segments with laser capture microdissection, created sequenced libraries generated tissues....
Genomics datasets are currently managed by iRODS, the Integrated Rule-Oriented Data System, which is an open source data management software. iRODS provides several services, including indexing, publishing, integrity, storage, and provenance. In this work, we investigate how NDN can seamlessly integrate into to provide simplified improved functionality such as name-based discovery, replication, retrieval, computation at edge. We show these based mechanisms well caching iRODs. Once completely...
Bigenic expression relationships are conventionally defined based on metrics such as Pearson or Spearman correlation that cannot typically detect latent, non-linear dependencies require the relationship to be monotonic. Further, combination of intrinsic and extrinsic noise well embedded between sample sub-populations reduces probability extracting biologically relevant edges during construction gene co-expression networks (GCNs). In this report, we address these problems via our NetExtractor...
Abstract Nodule number regulation in legumes is controlled by a feedback loop that integrates nutrient and rhizobia symbiont status signals to regulate nodule development. Signals from the roots are perceived shoot receptors, including CLV1-like receptor-like kinase known as SUNN annual medic Medicago truncatula . In absence of functional SUNN, autoregulation disrupted, resulting hypernodulation. To elucidate early mechanisms disrupted mutants, we searched for genes with altered expression...
Summary Legumes can establish a symbiotic relationship with nitrogen-fixing rhizobia by developing nodules after root exposure to lipo-chito-oligosaccharides secreted the bacteria. Nodule development initiates anticlinal mitotic divisions in pericycle and endodermal inner cortical cells, establishing cell lineages that ultimately form each nodule compartment. We characterized these isolating sequencing transcriptome of Medicago truncatula single nuclei derived from uninoculated roots...